Certificate Issued to multiple sites?

On our WHM server we can access the sites with the normally used domain names like example.com/ but if we try to access the same site with the fully qualified domain name (dot or root at the end ) like example.com./ the browser (Chrome) indicates in red that the site is not secure. When we look at the certificate information we find the certificate is issued to example.org. All of the sites on our server have this problem except of course example.org. By going to Home "SSL/TLS "Manage SSL Hosts I found that example.org is the "primary SSL website on the IP address". Our server is only using one IP address. While we haven't been getting any complains about not being able to use the fully qualified domain names we would like to fix this problem just so our sites work as they should. How can we do that?